Starting phenix.real_space_refine on Fri Aug 22 15:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb3_45413/08_2025/9cb3_45413.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3183 2.51 5 N 882 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4995 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3912 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 504} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 12, 'GLU:plan': 11, 'GLN:plan1': 5, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 153 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 967 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'GLU:plan': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 94 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG C 85 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 85 " occ=0.50 Time building chain proxies: 1.49, per 1000 atoms: 0.30 Number of scatterers: 4995 At special positions: 0 Unit cell: (77.655, 83.5, 97.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 902 8.00 N 882 7.00 C 3183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 206.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.684A pdb=" N PHE A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.929A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.988A pdb=" N VAL A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.671A pdb=" N PHE A 152 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 153 " --> pdb=" O TRP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 183 through 196 removed outlier: 4.088A pdb=" N LEU A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.510A pdb=" N GLU A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.725A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.668A pdb=" N LYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.647A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.644A pdb=" N GLN A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 324 Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.545A pdb=" N TRP A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.851A pdb=" N TYR A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.630A pdb=" N TYR A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.612A pdb=" N HIS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 485 through 498 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 518 through 523 removed outlier: 6.235A pdb=" N ARG A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.789A pdb=" N GLN A 527 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.954A pdb=" N LYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 96 through 111 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.778A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 157 293 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 2036 1.41 - 1.64: 3012 1.64 - 1.87: 36 1.87 - 2.10: 0 2.10 - 2.33: 1 Bond restraints: 5085 Sorted by residual: bond pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 1.331 2.335 -1.004 2.07e-02 2.33e+03 2.35e+03 bond pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 1.331 1.175 0.156 2.07e-02 2.33e+03 5.67e+01 bond pdb=" C SER A 77 " pdb=" O SER A 77 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.35e-02 5.49e+03 1.61e+01 bond pdb=" CA ALA A 76 " pdb=" CB ALA A 76 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.58e-02 4.01e+03 1.39e+01 bond pdb=" C SER A 77 " pdb=" N PHE A 78 " ideal model delta sigma weight residual 1.329 1.287 0.042 1.23e-02 6.61e+03 1.17e+01 ... (remaining 5080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.23: 6918 14.23 - 28.45: 1 28.45 - 42.68: 4 42.68 - 56.90: 1 56.90 - 71.13: 1 Bond angle restraints: 6925 Sorted by residual: angle pdb=" O GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 123.00 72.01 50.99 1.60e+00 3.91e-01 1.02e+03 angle pdb=" C GLY C 84 " pdb=" N AARG C 85 " pdb=" CA AARG C 85 " ideal model delta sigma weight residual 121.80 50.67 71.13 2.44e+00 1.68e-01 8.50e+02 angle pdb=" O GLY C 84 " pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 123.00 162.27 -39.27 1.60e+00 3.91e-01 6.02e+02 angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N BARG C 85 " ideal model delta sigma weight residual 116.20 78.13 38.07 2.00e+00 2.50e-01 3.62e+02 angle pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " ideal model delta sigma weight residual 116.20 153.14 -36.94 2.00e+00 2.50e-01 3.41e+02 ... (remaining 6920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 2927 35.98 - 71.97: 117 71.97 - 107.95: 6 107.95 - 143.93: 1 143.93 - 179.91: 1 Dihedral angle restraints: 3052 sinusoidal: 1073 harmonic: 1979 Sorted by residual: dihedral pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N AARG C 85 " pdb=" CA AARG C 85 " ideal model delta harmonic sigma weight residual 180.00 71.66 108.34 0 5.00e+00 4.00e-02 4.70e+02 dihedral pdb=" CD BARG C 85 " pdb=" NE BARG C 85 " pdb=" CZ BARG C 85 " pdb=" NH1BARG C 85 " ideal model delta sinusoidal sigma weight residual 0.00 179.91 -179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C ASN B 108 " pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" CB ASN B 108 " ideal model delta harmonic sigma weight residual -122.60 -110.00 -12.60 0 2.50e+00 1.60e-01 2.54e+01 ... (remaining 3049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 758 0.068 - 0.136: 61 0.136 - 0.205: 6 0.205 - 0.273: 4 0.273 - 0.341: 1 Chirality restraints: 830 Sorted by residual: chirality pdb=" CA ASN B 108 " pdb=" N ASN B 108 " pdb=" C ASN B 108 " pdb=" CB ASN B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE B 112 " pdb=" N ILE B 112 " pdb=" C ILE B 112 " pdb=" CB ILE B 112 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A 434 " pdb=" CB LEU A 434 " pdb=" CD1 LEU A 434 " pdb=" CD2 LEU A 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 827 not shown) Planarity restraints: 879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 84 " -0.127 2.00e-02 2.50e+03 1.43e-01 2.05e+02 pdb=" C GLY C 84 " 0.242 2.00e-02 2.50e+03 pdb=" O GLY C 84 " -0.044 2.00e-02 2.50e+03 pdb=" N AARG C 85 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 102 " 0.025 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C GLU B 102 " -0.085 2.00e-02 2.50e+03 pdb=" O GLU B 102 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 103 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 84 " -0.006 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C GLY C 84 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY C 84 " -0.029 2.00e-02 2.50e+03 pdb=" N BARG C 85 " -0.028 2.00e-02 2.50e+03 ... (remaining 876 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 2 2.01 - 2.74: 414 2.74 - 3.46: 7399 3.46 - 4.18: 10668 4.18 - 4.90: 19337 Nonbonded interactions: 37820 Sorted by model distance: nonbonded pdb=" C GLY C 84 " pdb=" CB AARG C 85 " model vdw 1.293 2.936 nonbonded pdb=" N GLY C 84 " pdb=" N BARG C 85 " model vdw 1.931 2.560 nonbonded pdb=" O GLY C 84 " pdb=" CB AARG C 85 " model vdw 2.196 3.440 nonbonded pdb=" OG SER A 158 " pdb=" O SER A 160 " model vdw 2.202 3.040 nonbonded pdb=" O TYR A 350 " pdb=" OH TYR A 385 " model vdw 2.244 3.040 ... (remaining 37815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.004 5085 Z= 0.741 Angle : 1.615 71.125 6925 Z= 0.857 Chirality : 0.046 0.341 830 Planarity : 0.007 0.143 879 Dihedral : 18.757 179.913 1756 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.46 % Allowed : 33.33 % Favored : 65.21 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.34), residues: 661 helix: 0.65 (0.26), residues: 451 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 461 TYR 0.017 0.002 TYR A 223 PHE 0.025 0.002 PHE A 210 TRP 0.018 0.002 TRP A 73 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.01490 ( 5085) covalent geometry : angle 1.61499 ( 6925) hydrogen bonds : bond 0.15545 ( 293) hydrogen bonds : angle 6.01486 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.229 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 81 average time/residue: 0.0764 time to fit residues: 8.2038 Evaluate side-chains 75 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.218897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151700 restraints weight = 12943.989| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 5.48 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5085 Z= 0.156 Angle : 0.652 14.128 6925 Z= 0.333 Chirality : 0.040 0.286 830 Planarity : 0.005 0.058 879 Dihedral : 8.327 179.124 719 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 6.25 % Allowed : 28.75 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.34), residues: 662 helix: 0.85 (0.25), residues: 459 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.022 0.002 TYR A 341 PHE 0.015 0.002 PHE B 101 TRP 0.013 0.001 TRP A 82 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5085) covalent geometry : angle 0.65151 ( 6925) hydrogen bonds : bond 0.04365 ( 293) hydrogen bonds : angle 4.37235 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 452 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7250 (tt) REVERT: A 486 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6536 (mp) outliers start: 29 outliers final: 15 residues processed: 100 average time/residue: 0.0657 time to fit residues: 8.7920 Evaluate side-chains 89 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.221480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157567 restraints weight = 8635.067| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 4.43 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5085 Z= 0.147 Angle : 0.616 11.635 6925 Z= 0.313 Chirality : 0.040 0.244 830 Planarity : 0.004 0.049 879 Dihedral : 8.155 179.645 718 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 6.88 % Allowed : 27.71 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.34), residues: 662 helix: 1.06 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 461 TYR 0.027 0.002 TYR A 341 PHE 0.012 0.002 PHE A 497 TRP 0.009 0.001 TRP B 61 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5085) covalent geometry : angle 0.61551 ( 6925) hydrogen bonds : bond 0.04046 ( 293) hydrogen bonds : angle 4.19602 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7197 (tp) cc_final: 0.6811 (mt) REVERT: A 204 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7920 (pp30) REVERT: A 239 ARG cc_start: 0.5013 (OUTLIER) cc_final: 0.4799 (mmp-170) REVERT: A 452 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7216 (tt) REVERT: A 486 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6490 (mp) REVERT: B 144 ASP cc_start: 0.7146 (m-30) cc_final: 0.6759 (m-30) outliers start: 32 outliers final: 22 residues processed: 94 average time/residue: 0.0781 time to fit residues: 9.5403 Evaluate side-chains 97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.216663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152364 restraints weight = 8631.638| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.40 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5085 Z= 0.194 Angle : 0.654 11.972 6925 Z= 0.330 Chirality : 0.041 0.236 830 Planarity : 0.005 0.047 879 Dihedral : 8.179 179.064 718 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 8.33 % Allowed : 28.54 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.33), residues: 662 helix: 0.86 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 461 TYR 0.032 0.003 TYR A 341 PHE 0.018 0.002 PHE A 433 TRP 0.010 0.002 TRP A 226 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 5085) covalent geometry : angle 0.65413 ( 6925) hydrogen bonds : bond 0.04497 ( 293) hydrogen bonds : angle 4.35052 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 182 HIS cc_start: 0.6210 (OUTLIER) cc_final: 0.5133 (t-90) REVERT: A 204 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7893 (pp30) REVERT: A 239 ARG cc_start: 0.5142 (OUTLIER) cc_final: 0.4877 (mmp-170) REVERT: A 287 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.5815 (t80) REVERT: A 379 TRP cc_start: 0.8190 (t60) cc_final: 0.7880 (t60) REVERT: A 486 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6630 (mp) REVERT: A 521 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6969 (ttp-110) REVERT: A 524 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: B 144 ASP cc_start: 0.7399 (m-30) cc_final: 0.7085 (m-30) outliers start: 39 outliers final: 25 residues processed: 103 average time/residue: 0.0734 time to fit residues: 9.9638 Evaluate side-chains 104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 50 optimal weight: 0.0270 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.221387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169774 restraints weight = 8276.789| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 4.69 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4008 r_free = 0.4008 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5085 Z= 0.124 Angle : 0.602 12.076 6925 Z= 0.297 Chirality : 0.039 0.204 830 Planarity : 0.004 0.048 879 Dihedral : 8.059 179.766 718 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.09 % Favored : 95.76 % Rotamer: Outliers : 7.08 % Allowed : 30.00 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.34), residues: 662 helix: 1.22 (0.26), residues: 453 sheet: None (None), residues: 0 loop : -0.96 (0.45), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 461 TYR 0.025 0.002 TYR A 341 PHE 0.014 0.001 PHE A 497 TRP 0.011 0.001 TRP A 82 HIS 0.003 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5085) covalent geometry : angle 0.60187 ( 6925) hydrogen bonds : bond 0.03528 ( 293) hydrogen bonds : angle 4.09998 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7247 (tp) cc_final: 0.6832 (mt) REVERT: A 204 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (pp30) REVERT: A 239 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4874 (mmp-170) REVERT: A 287 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5625 (t80) REVERT: A 379 TRP cc_start: 0.8137 (t60) cc_final: 0.7903 (t60) REVERT: A 452 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7373 (tt) REVERT: A 486 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6417 (mp) REVERT: A 524 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7586 (mp0) outliers start: 33 outliers final: 19 residues processed: 98 average time/residue: 0.0665 time to fit residues: 8.3338 Evaluate side-chains 97 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 84 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.219296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155093 restraints weight = 8413.056| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.41 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5085 Z= 0.133 Angle : 0.595 12.767 6925 Z= 0.291 Chirality : 0.039 0.203 830 Planarity : 0.005 0.047 879 Dihedral : 7.970 178.833 717 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.88 % Allowed : 29.58 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.35), residues: 662 helix: 1.28 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -0.99 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 461 TYR 0.026 0.002 TYR A 341 PHE 0.012 0.001 PHE A 433 TRP 0.008 0.001 TRP A 226 HIS 0.002 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5085) covalent geometry : angle 0.59507 ( 6925) hydrogen bonds : bond 0.03596 ( 293) hydrogen bonds : angle 4.00339 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7272 (tp) cc_final: 0.6871 (mt) REVERT: A 182 HIS cc_start: 0.6100 (OUTLIER) cc_final: 0.5053 (t-90) REVERT: A 239 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4864 (mmp-170) REVERT: A 287 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5744 (t80) REVERT: A 379 TRP cc_start: 0.8139 (t60) cc_final: 0.7885 (t60) REVERT: A 452 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7302 (tt) REVERT: A 486 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6547 (mp) REVERT: A 524 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 126 MET cc_start: 0.7694 (mmt) cc_final: 0.7436 (mtt) REVERT: B 144 ASP cc_start: 0.7349 (m-30) cc_final: 0.6957 (m-30) outliers start: 32 outliers final: 22 residues processed: 98 average time/residue: 0.0646 time to fit residues: 8.3807 Evaluate side-chains 101 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 6 optimal weight: 0.0270 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.220145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166540 restraints weight = 8524.782| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 4.48 r_work: 0.3732 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5085 Z= 0.123 Angle : 0.605 12.697 6925 Z= 0.290 Chirality : 0.039 0.246 830 Planarity : 0.004 0.047 879 Dihedral : 7.927 179.966 717 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.08 % Allowed : 30.00 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.35), residues: 662 helix: 1.38 (0.26), residues: 454 sheet: None (None), residues: 0 loop : -0.85 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 461 TYR 0.027 0.003 TYR A 341 PHE 0.010 0.001 PHE A 433 TRP 0.008 0.001 TRP A 73 HIS 0.002 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5085) covalent geometry : angle 0.60477 ( 6925) hydrogen bonds : bond 0.03434 ( 293) hydrogen bonds : angle 3.94599 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7360 (tp) cc_final: 0.6920 (mt) REVERT: A 182 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.4955 (t-90) REVERT: A 239 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.4849 (mmp-170) REVERT: A 287 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 379 TRP cc_start: 0.8130 (t60) cc_final: 0.7904 (t60) REVERT: A 452 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7280 (tt) REVERT: A 486 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6177 (mp) REVERT: A 524 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: B 126 MET cc_start: 0.7711 (mmt) cc_final: 0.7483 (mtt) REVERT: B 144 ASP cc_start: 0.7275 (m-30) cc_final: 0.6912 (m-30) outliers start: 33 outliers final: 24 residues processed: 100 average time/residue: 0.0685 time to fit residues: 8.8504 Evaluate side-chains 104 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.221274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152760 restraints weight = 12997.062| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 5.66 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5085 Z= 0.115 Angle : 0.599 12.770 6925 Z= 0.288 Chirality : 0.039 0.194 830 Planarity : 0.004 0.046 879 Dihedral : 7.844 179.767 717 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.08 % Allowed : 30.42 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.35), residues: 662 helix: 1.49 (0.26), residues: 453 sheet: None (None), residues: 0 loop : -0.80 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 461 TYR 0.029 0.002 TYR A 223 PHE 0.016 0.001 PHE A 497 TRP 0.008 0.001 TRP A 73 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5085) covalent geometry : angle 0.59861 ( 6925) hydrogen bonds : bond 0.03320 ( 293) hydrogen bonds : angle 3.86994 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1324 Ramachandran restraints generated. 662 Oldfield, 0 Emsley, 662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7271 (tp) cc_final: 0.6851 (mt) REVERT: A 182 HIS cc_start: 0.6111 (OUTLIER) cc_final: 0.5100 (t-90) REVERT: A 216 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: A 239 ARG cc_start: 0.5026 (OUTLIER) cc_final: 0.4783 (mmp-170) REVERT: A 287 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5596 (t80) REVERT: A 379 TRP cc_start: 0.8000 (t60) cc_final: 0.7791 (t60) REVERT: A 452 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7119 (tt) REVERT: A 486 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6478 (mp) REVERT: A 524 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 126 MET cc_start: 0.7586 (mmt) cc_final: 0.7253 (mtt) outliers start: 33 outliers final: 24 residues processed: 102 average time/residue: 0.0638 time to fit residues: 8.4069 Evaluate side-chains 105 residues out of total 591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 521 ARG Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 153 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9416 > 50: distance: 3 - 6: 22.590 distance: 6 - 7: 25.793 distance: 7 - 8: 17.800 distance: 7 - 10: 14.088 distance: 8 - 9: 26.071 distance: 8 - 11: 12.659 distance: 9 - 32: 26.949 distance: 11 - 12: 5.896 distance: 12 - 13: 14.058 distance: 12 - 15: 8.960 distance: 13 - 14: 22.708 distance: 13 - 20: 16.156 distance: 14 - 37: 10.563 distance: 15 - 16: 30.537 distance: 17 - 18: 14.385 distance: 17 - 19: 4.125 distance: 20 - 21: 11.060 distance: 21 - 22: 11.689 distance: 21 - 24: 16.847 distance: 22 - 23: 20.629 distance: 22 - 27: 3.601 distance: 24 - 25: 21.086 distance: 24 - 26: 15.649 distance: 27 - 28: 13.401 distance: 28 - 29: 8.974 distance: 28 - 31: 7.072 distance: 29 - 30: 7.209 distance: 29 - 32: 17.021 distance: 32 - 33: 16.650 distance: 33 - 34: 13.917 distance: 33 - 36: 10.002 distance: 34 - 35: 17.395 distance: 34 - 37: 13.366 distance: 37 - 38: 13.676 distance: 38 - 39: 10.985 distance: 38 - 41: 17.300 distance: 39 - 40: 8.526 distance: 39 - 44: 10.852 distance: 41 - 42: 20.516 distance: 41 - 43: 4.496 distance: 44 - 45: 18.510 distance: 45 - 46: 5.075 distance: 45 - 48: 13.293 distance: 46 - 47: 19.258 distance: 46 - 53: 19.224 distance: 48 - 49: 7.613 distance: 49 - 50: 16.658 distance: 50 - 51: 17.352 distance: 50 - 52: 21.873 distance: 53 - 54: 16.964 distance: 54 - 55: 33.705 distance: 54 - 57: 11.701 distance: 55 - 56: 29.122 distance: 55 - 58: 23.386 distance: 58 - 59: 7.282 distance: 59 - 60: 22.028 distance: 60 - 61: 33.182 distance: 60 - 62: 15.051 distance: 62 - 63: 8.240 distance: 63 - 64: 6.150 distance: 63 - 66: 21.335 distance: 64 - 70: 3.555 distance: 66 - 67: 15.513 distance: 67 - 68: 10.661 distance: 67 - 69: 14.454